Hi !
NAMD can read AMBER topology files which store all the needed
information for the system. As long as your topology contains the
correct connectivity information, chain or segment IDs are not relevant
and everything should be fine from that point of view.
Just read the documentation carefully. Some NAMD inputs need to be
adjusted from their defaults ...
The Wiki below was written for earlier versions of both NAMD and AMBER
but the basics have not changed. It is the best explanation I am aware
of about using the Amber force fields in NAMD. Nevertheless, double
check parameters and defaults in newer versions to be sure you are doing
things right.
https://ambermd.org/namd/namd_amber.html
Cheers
Vlad
On 4/6/22 12:03, Hrishikesh Dhondge wrote:
> Hello,
>
> I have a doubt regarding the use of the amber force field with NAMD. If I
> have to use the amber force field in NAMD, then I can create the system in
> the leap program provided by AMBER. But the leap program renumbers the
> residues in the simulation system. Chain identifiers are not used. There is
> a single list of all atoms where atoms and residues are numbered
> sequentially starting from 1 without any gaps.
>
> So if I have a protein-RNA/DNA complex to simulate, will it affect the
> simulation (missing information about chain or segment identifiers)?
>
> Thanks in advance!
>
--
Vlad Cojocaru, PD (Habil.), Ph.D.
-----------------------------------------------
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
-----------------------------------------------
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Wed Apr 06 2022 - 05:30:02 PDT
